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*Assumes the file is sorted by Coordinate (or ReadName if using <code>--readName</code> option)
*Assumes the file is sorted by Coordinate (or ReadName if using <code>--readName</code> option)
*Assumes only 2 reads have matching ReadNames
*Assumes only 2 reads have matching ReadNames (Supplementary and Secondary reads are ignored/skipped by default so will not cause a problem)
**It matches in pairs, so if there are 3, the first 2 will be matched and compared, but the 3rd won't. If there are 4, the first 2 will be matched and the last 2 will be matched and compared.
**It matches in pairs, so if there are 3, the first 2 will be matched and compared, but the 3rd won't. If there are 4, the first 2 will be matched and the last 2 will be matched and compared.
*Only mapped reads will be clipped
*Only mapped reads will be clipped
--stats : Print some statistics on the overlaps.
--stats : Print some statistics on the overlaps.
--overlapsOnly : Only output overlapping read pairs
--overlapsOnly : Only output overlapping read pairs
--excludeFlags : Skip records with any of the specified flags set, default 0x70C
--excludeFlags : Skip records with any of the specified flags set, default 0xF0C
--unmapped : Mark records that would be completely clipped as unmapped
--unmapped : Mark records that would be completely clipped as unmapped
--noeof : Do not expect an EOF block on a bam file.
--noeof : Do not expect an EOF block on a bam file.
=== Skip Records with any of the Specified Flags (<code>--excludeFlags</code>)===
=== Skip Records with any of the Specified Flags (<code>--excludeFlags</code>)===
Skip records with any of the specified flags set, default 0x70C
Skip records with any of the specified flags set, default 0xF0C
By default skips reads with any of the following flags set:
By default skips reads with any of the following flags set:
* fails QC checks
* fails QC checks
* duplicate
* duplicate
* supplementary
=== Mark entirely clipped reads as unmapped (<code>--unmapped</code>)===
=== Mark entirely clipped reads as unmapped (<code>--unmapped</code>)===
